PE-Assembler specifications

Information


Unique identifier OMICS_00025
Name PE-Assembler
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.2
Stability Stable
Maintained Yes

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Publication for PE-Assembler

PE-Assembler in publications

 (4)
PMCID: 4562602
PMID: 26348928
DOI: 10.1371/journal.pone.0137526

[…] size of the dna-pet libraries). this corresponded to 1,031 locations. we also split scaffolds at cpets coverage breakpoints (see above). the two datasets were then combined and processed with the pe-assembler software [], which was previously shown to perform well (see , []). the statistics of the improved assembly are shown in . the total number of scaffolds is reduced by 56%, the n50 […]

PMCID: 3990616
PMID: 24743507
DOI: 10.1371/journal.pone.0095057

[…] chemistry., the sequencing data were filtered and paired reads removed if more than five ambiguous bases were present in either read. the reads were then assembled in a single pool by the abyss-pe assembler (v1.27, simpson, et al., 2009 ) and manipulated in the geneious sequence workbench (v5, ), including identification and extraction of orfs. sequences were aligned to 100 kb segments […]

PMCID: 3469383
PMID: 22884033
DOI: 10.1186/1471-2164-13-385

[…] terminators accordingly to illumina, inc., low quality reads produced by the illumina gaiix method were filtered using the shortread 1.8.0 package []. assembly for each strain was performed with the pe-assembler 1.1 []. image 2.1 [] was used to close gaps as it locally assembles reads aligning to contig ends. bowtie 0.12.5 short read aligner [] was used to align reads to the resulting contigs […]

PMCID: 2945791
PMID: 20799932
DOI: 10.1186/gb-2010-11-8-r89

[…] repeats were excluded. functional classification of snps was performed using gene co-ordinates from the bte264 reference genome. de novo assembly of the bte555 paired-end reads was performed using pe-assembler, an in-house toolkit (pa and ws, manuscript in preparation). de novo assembled contigs were mapped to the reference bt e264 genome using nucmer [] and contig aligner []. genes on contigs […]


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PE-Assembler institution(s)
Computational & Mathematical Biology Group, Genome Institute of Singapore, Singapore; School of Computing, National University of Singapore, Singapore
PE-Assembler funding source(s)
Supported by MOE AcRF Tier 2 funding R-252-000-444-112 and Agency for Science, Technology and Research (A*STAR).

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